The correct way to 'rewire' the ribbon cable is to redesign the motherboard or to use the correct ribbon cable and adapter. Don't open the long, fragile plastic 40 pin connectors on the ribbon cables unless you want to replace them. If there is a way to open those without causing possible problems, let me know.
For other ribbon cables like those for an additional parallel or serial port or other interface, only make changes carefully. Since the ribbon cable is connected to the mb interface and their pins and ends with its own ext device connector, if the mb interface does conform to any particular standard, the resulting ext device connector must also be non-standard in it's wiring to result in final pins with correct voltages for the device.
Yes, I've done what you say before, but at the end ext device connector, not the mb interface connector. The only reason that I could do this is that a different ribbon cable was used that was pin identical, but different in wiring. So I had to make them match.